Mesh generation is a bottleneck for finite element simulations of biomolecules. A robust and efficient approach, based on the immersed boundary method proposed in [8], has been developed and implemented to generate large-scale mesh body-fitted to molecular shape for general parallel finite element simulations. The molecular Gaussian surface is adopted to represent the molecular surface, and is finally approximated by piecewise planes via the tool phgSurfaceCut in PHG [43], which is improved and can reliably handle complicated molecular surfaces, through mesh refinement steps. A coarse background mesh is imported first and then is distributed into each process using a mesh partitioning algorithm such as space filling curve [5] or METIS [22]. A bisection method is used for the mesh refinements according to the molecular PDB or PQR file which describes the biomolecular region. After mesh refinements, the mesh is optionally repartitioned and redistributed for load balancing. For finite element simulations, the modification of region mark and boundary types is done in parallel. Our parallel mesh generation method has been successfully applied to a sphere cavity model, a DNA fragment, a gramicidin A channel and a huge Dengue virus system. The results of numerical experiments show good parallel efficiency. Computations of electrostatic potential and solvation energy also validate the method. Moreover, the meshing process and adaptive finite element computation can be integrated as one PHG project to avoid the mesh importing and exporting costs, and improve the convenience of application as well.

The lobe dynamics andmass transport between separation bubble and main flow in flow over airfoil are studied in detail, using Lagrangian coherent structures (LCSs), in order to understand the nature of evolution of the separation bubble. For this problem, the transient flow over NACA0012 airfoil with low Reynolds number is simulated numerically by characteristic based split (CBS) scheme, in combination with dual time stepping. Then, LCSs and lobe dynamics are introduced and developed to investigate themass transport between separation bubble and main flow, from viewpoint of nonlinear dynamics. The results show that stable manifolds and unstable manifolds could be tangled with each other as time evolution, and the lobes are formed periodically to induce mass transport between main flow and separation bubble, with dynamic behaviors. Moreover, the evolution of the separation bubble depends essentially on the mass transport which is induced by lobes, ensuing energy and momentum transfers. As the results, it can be drawn that the dynamics of flow separation could be studied using LCSs and lobe dynamics, and could be controlled feasibly if an appropriate control is applied to the upstream boundary layer with high momentum.

We consider the dynamics of the director in a nematic liquid crystal when under the influence of an applied electric field. Using an energy variational approach we derive a dynamic model for the director including both dissipative and inertial forces.

A numerical scheme for the model is proposed by extending a scheme for a related variational wave equation. Numerical experiments are performed studying the realignment of the director field when applying a voltage difference over the liquid crystal cell. In particular, we study how the relative strength of dissipative versus inertial forces influence the time scales of the transition between the initial configuration and the electrostatic equilibrium state.

A two-dimensional numerical scheme for the compressible Euler equations is presented and applied here to the simulation of exemplary compressible vortical flows. The proposed approach allows to perform computations on unstructured moving grids with adaptation, which is required to capture complex features of the flow-field. Grid adaptation is driven by suitable error indicators based on the Mach number and by element-quality constraints as well. At the new time level, the computational grid is obtained by a suitable combination of grid smoothing, edge-swapping, grid refinement and de-refinement. The grid modifications—including topology modification due to edge-swapping or the insertion/deletion of a new grid node—are interpreted at the flow solver level as continuous (in time) deformations of suitably-defined node-centered finite volumes. The solution over the new grid is obtained without explicitly resorting to interpolation techniques, since the definition of suitable interface velocities allows one to determine the new solution by simple integration of the Arbitrary Lagrangian-Eulerian formulation of the flow equations. Numerical simulations of the steady oblique-shock problem, of the steady transonic flow and of the start-up unsteady flow around the NACA 0012 airfoil are presented to assess the scheme capabilities to describe these flows accurately.

In the present work adaptation in meshless framework is proposed. The grid adaptation or mesh adaptation is quite well developed area in case of conventional grid based solvers and is popularly known as Adaptive mesh refinement (AMR). In such cases the adaptation is done by subdividing the cells or elements into finer cells or elements. In case of meshless methods there are no cells or elements but only a cloud of points. In this work we propose to achieve the meshless adaptation by locally refining the point density in the regions demanding higher resolution. This results into an adaptive enriched cloud of points. We call this method as Adaptive Cloud Refinement (ACR). The meshless solvers need connectivity information, which is a set of neighboring nodes. It is crucial part of meshless solvers. Obviously because of refining point density, the connectivity of nodes in such regions gets modified and hence has to be updated. An efficient connectivity update must exploit the fact that the node distribution would be largely unaffected except the region of adaptation. Hence connectivity updating needs to be done locally, only in these regions. In this paper we also present an extremely fast algorithm to update connectivity over adapted cloud called as ACU (Automatic Connectivity Update).

In this article, we present two new novel finite difference approximations of order two and four, respectively, for the three dimensional non-linear triharmonic partial differential equations on a compact stencil where the values of u, ∂2u/∂n2 and ∂4u/∂n4 are prescribed on the boundary. We introduce new ideas to handle the boundary conditions and there is no need to discretize the derivative boundary conditions. We require only 7- and 19-grid points on the compact cell for the second and fourth order approximation, respectively. The Laplacian and the biharmonic of the solution are obtained as by-product of the methods. We require only system of three equations to obtain the solution. Numerical results are provided to illustrate the usefulness of the proposed methods.

The probabilistic solutions of the nonlinear stochastic dynamic (NSD) systems with polynomial type of nonlinearity are investigated with the subspace-EPC method. The space of the state variables of large-scale nonlinear stochastic dynamic system excited by white noises is separated into two subspaces. Both sides of the Fokker-Planck-Kolmogorov (FPK) equation corresponding to the NSD system is then integrated over one of the subspaces. The FPK equation for the joint probability density function of the state variables in another subspace is formulated. Therefore, the FPK equation in low dimensions is obtained from the original FPK equation in high dimensions and it makes the problem of obtaining the probabilistic solutions of large-scale NSD systems solvable with the exponential polynomial closure method. Examples about the NSD systems with polynomial type of nonlinearity are given to show the effectiveness of the subspace-EPC method in these cases.

We study a novel class of numerical integrators, the adapted nested force-gradient schemes, used within the molecular dynamics step of the Hybrid Monte Carlo (HMC) algorithm. We test these methods in the Schwinger model on the lattice, a well known benchmark problem. We derive the analytical basis of nested force-gradient type methods and demonstrate the advantage of the proposed approach, namely reduced computational costs compared with other numerical integration schemes in HMC.

Hermite methods, as introduced by Goodrich et al. in [15], combine Hermite interpolation and staggered (dual) grids to produce stable high order accurate schemes for the solution of hyperbolic PDEs. We introduce three variations of this Hermite method which do not involve time evolution on dual grids. Computational evidence is presented regarding stability, high order convergence, and dispersion/dissipation properties for each new method. Hermite methods may also be coupled to discontinuous Galerkin (DG) methods for additional geometric flexibility [4]. An example illustrates the simplification of this coupling for Hermite methods.

A new representation of spatio-temporal random processes is proposed in this work. In practical applications, such processes are used to model velocity fields, temperature distributions, response of vibrating systems, to name a few. Finding an efficient representation for any random process leads to encapsulation of information which makes it more convenient for a practical implementations, for instance, in a computational mechanics problem. For a single-parameter process such as spatial or temporal process, the eigenvalue decomposition of the covariance matrix leads to the well-known Karhunen-Loève (KL) decomposition. However, for multiparameter processes such as a spatio-temporal process, the covariance function itself can be defined in multiple ways. Here the process is assumed to be measured at a finite set of spatial locations and a finite number of time instants. Then the spatial covariance matrix at different time instants are considered to define the covariance of the process. This set of square, symmetric, positive semi-definite matrices is then represented as a third-order tensor. A suitable decomposition of this tensor can identify the dominant components of the process, and these components are then used to define a closed-form representation of the process. The procedure is analogous to the KL decomposition for a single-parameter process, however, the decompositions and interpretations vary significantly. The tensor decompositions are successfully applied on (i) a heat conduction problem, (ii) a vibration problem, and (iii) a covariance function taken from the literature that was fitted to model a measured wind velocity data. It is observed that the proposed representation provides an efficient approximation to some processes. Furthermore, a comparison with KL decomposition showed that the proposed method is computationally cheaper than the KL, both in terms of computer memory and execution time.

In this article, we consider a domain consisting of two cavities linked by a hole of small size. We derive a numerical method to compute an approximation of the eigenvalues of an elliptic operator without refining in the neighborhood of the hole. Several convergence rates are obtained and illustrated by numerical simulations.

We study pseudo-arclength continuation methods for both Rydberg-dressed Bose-Einstein condensates (BEC), and binary Rydberg-dressed BEC which are governed by the Gross-Pitaevskii equations (GPEs). A divide-and-conquer technique is proposed for rescaling the range/ranges of nonlocal nonlinear term/terms, which gives enough information for choosing a proper stepsize. This guarantees that the solution curve we wish to trace can be precisely approximated. In addition, the ground state solution would successfully evolve from one peak to vortices when the affect of the rotating term is imposed. Moreover, parameter variables with different number of components are exploited in curve-tracing. The proposed methods have the advantage of tracing the ground state solution curve once to compute the contours for various values of the coefficients of the nonlocal nonlinear term/terms. Our numerical results are consistent with those published in the literatures.

We propose and analyse finite volume Godunov type methods based on discontinuous flux for a 2×2 system of non-linear partial differential equations proposed by Hadeler and Kuttler to model the dynamics of growing sandpiles generated by a vertical source on a flat bounded rectangular table. The problem considered here is the so-called partially open table problem where sand is blocked by a wall (of infinite height) on some part of the boundary of the table. The novelty here is the corresponding modification of boundary conditions for the standing and the rolling layers and generalization of the techniques of the well-balancedness proposed in [1]. Presence of walls may lead to unbounded or discontinuous surface flow density at equilibrium resulting in solutions with singularities propagating from the extreme points of the walls. A scheme has been proposed to approximate efficiently the Hamiltonians with the coefficients which can be unbounded and discontinuous. Numerical experiments are presented to illustrate that the proposed schemes detect these singularities in the equilibrium solutions efficiently and comparisons are made with the previously studied finite difference and Semi-Lagrangian approaches by Finzi Vita et al.

In this paper, we propose a novel and simple technique to construct effective difference schemes for solving systems of singularly perturbed convection-diffusion-reaction equations, whose solutions may display boundary or interior layers. We illustrate the technique by taking the Il'in-Allen-Southwell scheme for 1-D scalar equations as a basis to derive a formally second-order scheme for 1-D coupled systems and then extend the scheme to 2-D case by employing an alternating direction approach. Numerical examples are given to demonstrate the high performance of the obtained scheme on uniform meshes as well as piecewise-uniform Shishkin meshes.

In the first of a series of papers, we will study a discontinuous Galerkin (DG) framework for many electron quantum systems. The salient feature of this framework is the flexibility of using hybrid physics-based local orbitals and accuracy-guaranteed piecewise polynomial basis in representing the Hamiltonian of the many body system. Such a flexibility is made possible by using the discontinuous Galerkin method to approximate the Hamiltonian matrix elements with proper constructions of numerical DG fluxes at the finite element interfaces. In this paper, we will apply the DG method to the density matrix minimization formulation, a popular approach in the density functional theory of many body Schrödinger equations. The density matrix minimization is to find the minima of the total energy, expressed as a functional of the density matrix ρ(r,r′), approximated by the proposed enriched basis, together with two constraints of idempotency and electric neutrality. The idempotency will be handled with the McWeeny’s purification while the neutrality is enforced by imposing the number of electrons with a penalty method. A conjugate gradient method (a Polak-Ribiere variant) is used to solve the minimization problem. Finally, the linear-scaling algorithm and the advantage of using the local orbital enriched finite element basis in the DG approximations are verified by studying examples of one dimensional lattice model systems.

In this paper, we revisit the Nested Stochastic Simulation Algorithm (NSSA) for stochastic chemical reacting networks by first proving its strong convergence. We then study a speed up of the algorithm by using the explicit Tau-Leaping method as the Inner solver to approximate invariant measures of fast processes, for which strong error estimates can also be obtained. Numerical experiments are presented to demonstrate the validity of our analysis.

The low temperature properties of double exchange model in triangular lattice are investigated via truncated polynomial expansion method (TPEM), which reduces the computational complexity and enables parallel computation. We found that for the half-filling case a stable 120° spin configuration phase occurs owing to the frustration of triangular lattice and is further stabilized by antiferromagnetic (AF) su-perexchange interaction, while a transition between a stable ferromagnetic (FM) phase and a unique flux phase with small finite-size effect is induced by AF superexchange interaction for the quarter-filling case.

In this paper, we study high order discretization methods for solving the Maxwell equations on hybrid triangle-quad meshes. We have developed high order finite edge element methods coupled with different high order time schemes and we compare results and efficiency for several schemes. We introduce in particular a class of simple high order low dissipation time schemes based on a modified Taylor expansion.

It is well known that grid discontinuities have significant impact on the performance of finite difference schemes (FDSs). The geometric conservation law (GCL) is very important for FDSs on reducing numerical oscillations and ensuring free-stream preservation in curvilinear coordinate system. It is not quite clear how GCL works in finite difference method and how GCL errors affect spatial discretization errors especially in nonsmooth grids. In this paper, a method is developed to analyze the impact of grid discontinuities on the GCL errors and spatial discretization errors. A violation of GCL cause GCL errors which depend on grid smoothness, grid metrics method and finite difference operators. As a result there are more source terms in spatial discretization errors. The analysis shows that the spatial discretization accuracy on non-sufficiently smooth grids is determined by the discontinuity order of grids and can approach one higher order by following GCL. For sufficiently smooth grids, the spatial discretization accuracy is determined by the order of FDSs and FDSs satisfying the GCL can obtain smaller spatial discretization errors. Numerical tests have been done by the second-order and fourth-order FDSs to verify the theoretical results.

Because of stability constraints, most numerical schemes applied to hyperbolic systems of equations turn out to be costly when the flux term is multiplied by some very large scalar. This problem emerges with the M1 system of equations in the field of radiotherapy when considering heterogeneous media with very disparate densities. Additionally, the flux term of the M1 system is non-linear, and in order for the model to be well-posed the numerical solution needs to fulfill conditions called realizability. In this paper, we propose a numerical method that overcomes the stability constraint and preserves the realizability property. For this purpose, we relax the M1 system to obtain a linear flux term. Then we extend the stencil of the difference quotient to obtain stability. The scheme is applied to a radiotherapy dose calculation example.